Computational analysis of sodium-dependent phosphate transporter SLC20A1/PiT1 gene identifies missense variations C573F, and T58A as high-risk deleterious SNPs

Abstract

SLC20A1/PiT1 is a sodium-dependent inorganic phosphate transporter, initially recognized as the retroviral receptor for Gibbon Ape Leukemia Virus in humans. SNPs in SLC20A1 is associated with Combined Pituitary Hormone Deficiency and Sodium Lithium Counter transport. Using in silico techniques, we have screened the nsSNPs for their deleterious effect on the structure and function of SLC20A1. Screening with sequence and structure-based tools on 430 nsSNPs, filtered 17 nsSNPs which are deleterious. To evaluate the role of these SNPs, protein modeling and MD simulations were performed. A comparative analysis of model generated with SWISS-MODEL and AlphaFold shows that many residues are in the disallowed region of Ramachandran plot. Since SWISS-MODEL structure has a 25-residue deletion, the AlphaFold structure was used to perform MD simulation for equilibration and structure refinement. Further, to understand perturbation of energetics, we performed in silico mutagenesis and ΔΔG calculation using FoldX on MD refined structures, which yielded SNPs that are neutral (3), destabilizing (12) and stabilizing (2) on protein structure. Furthermore, to elucidate the impact of SNPs on structure, we performed MD simulations to discern the changes in RMSD, Rg, RMSF and LigPlot of interacting residues. RMSF profiles of representative SNPs revealed that A114V (neutral) and T58A (positive) were more flexible & C573F (negative) was more rigid compared to wild type, which is also reflected in the changes in number of local interacting residues in LigPlot and ΔΔG. Taken together, our results show that SNPs can lead to structural perturbations and impact the function of SLC20A1 with potential implications for disease.

Communicated by Ramaswamy H. Sarma

Keywords:

• SLC20A1
• RMSD
• missense
• non-synonymous
• RMSF
• LIG plot
• molecular dynamics

Acknowledgement

We would like to thank Rajesh Michael for his valuable insights provided during manuscript preparation. We thank Center for Computational Science & Molecular Modeling Simulation (COSMOS) Lab from Central Research Instruments Facility (CRIF), SSSIHL for providing the computational resources to perform molecular dynamics simulations.

Authors’ contributions

The work was designed and formulated by SSG, SKS and RJ. MD Simulation studies was designed and executed by SK, VS and VKTV. Manuscript was prepared by SSG, RJ, FP, SK and VKTV. All authors reviewed and revised the manuscript.

Disclosure statement

The authors declare that there is no conflict of interest regarding the publication of this article.

Funding

The authors did not receive any kind of financial support for the submitted work.

Data availability statement

The data used to support the findings of this study are available from the corresponding authors upon request.